Jumping Alignments (JAli)is an alignment method for comparing a protein sequence to a protein family,
represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is ]
a generalization of the Smith-Watherman algorithm.

The Project contains three parts:

jali - jali takes as input a protein sequence and a multiple alignment of a
protein family and computes a jumping alignment of the sequence and the alignment.

jsearch(no online version available) - jsearch takes as input a protein database
and a multipe alignment of a protein family, compares all proteins from the database to the alignment, and then
outputs the database in sorted order with respect to the computed jumping alignment score.

jscan(no online version available) -jscan takes as input a protein sequence and a
database of multiple alignments of protein sequences (PRODOM format). jscan computes a jumping alignment for the
sequence and each multiple alignment from the database, and then outputs the cluster names in sorted order with
respect to the computed jumping alignment score.